Add proper protocols documentation

[andrea-pasquale]

This PR aims at providing a comprehensible documentation for all protocols available in qibocal.

TODOs:

• [x] Use autoclass to show Parameters in the same page
• [x] Add single page with references

Protocols:

• [x] qubit spectroscopy
• [x] qubit spectroscopy ef
• [x] ramsey
• [x] ramsey signal
• [x] t1
• [x] t1_signal
• [x] t1_sequences
• [x] t2
• [x] t2_signal
• [x] t2_sequences
• [x] kernel
• [x] tof
• [x] qubit_flux_dependence
• [x] resonator_flux_dependence
• [x] qubit_tracking
• [x] rabis #868
• [x] single shots #868
• [x] dispersive shift #868
• [x] flipping #868
• [x] allxy #868

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 97.32%. Comparing base (b0c0ef7) to head (ab4e61b). Report is 64 commits behind head on main.

Additional details and impacted files

[](https://app.codecov.io/gh/qiboteam/qibocal/pull/861?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam) ```diff @@ Coverage Diff @@ ## main #861 +/- ## ========================================== - Coverage 97.40% 97.32% -0.09% ========================================== Files 115 115 Lines 8645 8645 ========================================== - Hits 8421 8414 -7 - Misses 224 231 +7 ``` | [Flag](https://app.codecov.io/gh/qiboteam/qibocal/pull/861/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/qiboteam/qibocal/pull/861/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam) | `97.32% <100.00%> (-0.09%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files](https://app.codecov.io/gh/qiboteam/qibocal/pull/861?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam) | Coverage Δ | | |---|---|---| | [src/qibocal/protocols/classification.py](https://app.codecov.io/gh/qiboteam/qibocal/pull/861?src=pr&el=tree&filepath=src%2Fqibocal%2Fprotocols%2Fclassification.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam#diff-c3JjL3FpYm9jYWwvcHJvdG9jb2xzL2NsYXNzaWZpY2F0aW9uLnB5) | `100.00% <ø> (ø)` | | | [src/qibocal/protocols/coherence/t2.py](https://app.codecov.io/gh/qiboteam/qibocal/pull/861?src=pr&el=tree&filepath=src%2Fqibocal%2Fprotocols%2Fcoherence%2Ft2.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam#diff-c3JjL3FpYm9jYWwvcHJvdG9jb2xzL2NvaGVyZW5jZS90Mi5weQ==) | `94.02% <ø> (ø)` | | | [src/qibocal/protocols/coherence/t2\_signal.py](https://app.codecov.io/gh/qiboteam/qibocal/pull/861?src=pr&el=tree&filepath=src%2Fqibocal%2Fprotocols%2Fcoherence%2Ft2_signal.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam#diff-c3JjL3FpYm9jYWwvcHJvdG9jb2xzL2NvaGVyZW5jZS90Ml9zaWduYWwucHk=) | `100.00% <ø> (ø)` | | | [src/qibocal/protocols/qubit\_spectroscopy\_ef.py](https://app.codecov.io/gh/qiboteam/qibocal/pull/861?src=pr&el=tree&filepath=src%2Fqibocal%2Fprotocols%2Fqubit_spectroscopy_ef.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam#diff-c3JjL3FpYm9jYWwvcHJvdG9jb2xzL3F1Yml0X3NwZWN0cm9zY29weV9lZi5weQ==) | `98.52% <100.00%> (ø)` | | | [src/qibocal/protocols/ramsey/ramsey.py](https://app.codecov.io/gh/qiboteam/qibocal/pull/861?src=pr&el=tree&filepath=src%2Fqibocal%2Fprotocols%2Framsey%2Framsey.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam#diff-c3JjL3FpYm9jYWwvcHJvdG9jb2xzL3JhbXNleS9yYW1zZXkucHk=) | `99.08% <ø> (ø)` | | | [src/qibocal/protocols/ramsey/ramsey\_signal.py](https://app.codecov.io/gh/qiboteam/qibocal/pull/861?src=pr&el=tree&filepath=src%2Fqibocal%2Fprotocols%2Framsey%2Framsey_signal.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam#diff-c3JjL3FpYm9jYWwvcHJvdG9jb2xzL3JhbXNleS9yYW1zZXlfc2lnbmFsLnB5) | `97.63% <ø> (ø)` | | ... and [3 files with indirect coverage changes](https://app.codecov.io/gh/qiboteam/qibocal/pull/861/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=qiboteam)

[rodolfocarobene]

Thanks @andrea-pasquale and @Edoardo-Pedicillo! When compiling the documentation, when a protocol has the bibliography there is some layout problem and sphinx complains that entries are repeated... A possible solution could maybe to have a single page with all the references (?) not sure

[andrea-pasquale]

Thanks @andrea-pasquale and @Edoardo-Pedicillo! When compiling the documentation, when a protocol has the bibliography there is some layout problem and sphinx complains that entries are repeated... A possible solution could maybe to have a single page with all the references (?) not sure

Yes, we know. We are planning to move to a single page with all references. I'm not sure if this will fix the issue. We need to have a look into sphinx.

[andrea-pasquale]

Apart from some missing figures I don't think that I am planning to change anything else related to the protocols currently documented in this PR. In the last updates I have included:

• autoclass to show parameters
• add a single page with all references
• add requirements section to all protocols

Feel free to have a look @Edoardo-Pedicillo @rodolfocarobene @alecandido Even if the documentation for each experiment is not perfect, as agreed already today, I would like to merge this by Friday as an "initial" documentation that people can ready without having to build the documentation locally :)

[andrea-pasquale]

@rodolfocarobene @Edoardo-Pedicillo if you have further comments let me know. I would like to merge this PR today.

[andrea-pasquale]

I'll merge now. Thanks everyone for contributing and reviewing.